Epigenetics and T-cell immunity

References

• Reik W, Dean W, Walter J. Epigenetic reprogramming in mammalian development. Science 2001; 293: 1089–1093
   PubMed Web of Science ®Google Scholar
• Li E, Beard C, Jaenisch R. Role for DNA methylation in genomic imprinting. Nature 1993; 366: 362–365
   PubMed Web of Science ®Google Scholar
• Mohandas T, Sparkes RS, Shapiro LJ. Reactivation of an inactive human X chromosome: Evidence for X inactivation by DNA methylation. Science 1981; 211: 393–396
   PubMed Web of Science ®Google Scholar
• Bird AP. Functions for DNA methylation in vertebrates. Cold Spring Harb Symp Quant Biol 1993; 58: 281–285
   PubMedGoogle Scholar
• Egger G, Liang G, Aparicio A, Jones PA. Epigenetics in human disease and prospects for epigenetic therapy. Nature 2004; 429: 457–463
   PubMed Web of Science ®Google Scholar
• Razin A, Riggs AD. DNA methylation and gene function. Science 1980; 210: 604–610
   PubMed Web of Science ®Google Scholar
• Riggs AD. X inactivation, differentiation, and DNA methylation. Cytogenet Cell Genet 1975; 14: 9–25
   PubMedGoogle Scholar
• Bird AP. Use of restriction enzymes to study eukaryotic DNA methylation: II. The symmetry of methylated sites supports semi-conservative copying of the methylation pattern. J Mol Biol 1978; 118: 49–60
   PubMed Web of Science ®Google Scholar
• Holliday R, Pugh JE. DNA modification mechanisms and gene activity during development. Science 1975; 187: 226–232
   PubMed Web of Science ®Google Scholar
• Okano M, Bell DW, Haber DA, Li E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 1999; 99: 247–257
   PubMed Web of Science ®Google Scholar
• Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J Mol Biol 1987; 196: 261–282
   PubMed Web of Science ®Google Scholar
• Sutter D, Doerfler W. Methylation of integrated adenovirus type 12 DNA sequences in transformed cells is inversely correlated with viral gene expression. Proc Natl Acad Sci USA 1980; 77: 253–256
   PubMed Web of Science ®Google Scholar
• Bird AP, Wolffe AP. Methylation-induced repression—belts, braces, and chromatin. Cell 1999; 99: 451–454
   PubMed Web of Science ®Google Scholar
• Nan X, Ng HH, Johnson CA, Laherty CD, Turner BM, Eisenman RN, Bird A. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 1998; 393: 386–389
   PubMed Web of Science ®Google Scholar
• Jones PL, Veenstra GJ, Wade PA, Vermaak D, Kass SU, Landsberger N, Strouboulis J, Wolffe AP. Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat Genet 1998; 19: 187–191
   PubMed Web of Science ®Google Scholar
• Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 1997; 389: 251–260
   PubMed Web of Science ®Google Scholar
• Strahl BD, Allis CD. The language of covalent histone modifications. Nature 2000; 403: 41–45
   PubMed Web of Science ®Google Scholar
• Jenuwein T, Allis CD. Translating the histone code. Science 2001; 293: 1074–1080
   PubMed Web of Science ®Google Scholar
• Peterson CL, Laniel MA. Histones and histone modifications. Curr Biol 2004; 14: R546–R551
   PubMed Web of Science ®Google Scholar
• Garcia-Ramirez M, Rocchini C, Ausio J. Modulation of chromatin folding by histone acetylation. J Biol Chem 1995; 270: 17923–17928
   PubMed Web of Science ®Google Scholar
• Mosmann TR, Cherwinski H, Bond MW, Giedlin MA, Coffman RL. Two types of murine helper T cell clone I. Definition according to profiles of lymphokine activities and secreted proteins. J Immunol 1986; 136: 2348–2357
   PubMed Web of Science ®Google Scholar
• Cher DJ, Mosmann TR. Two types of murine helper T cell clone. II. Delayed-type hypersensitivity is mediated by TH1 clones. J Immunol 1987; 138: 3688–3694
   PubMed Web of Science ®Google Scholar
• Abbas AK, Murphy KM, Sher A. Functional diversity of helper T lymphocytes. Nature 1996; 383: 787–793
   PubMed Web of Science ®Google Scholar
• Robinson DS, Hamid Q, Ying S, Tsicopoulos A, Barkans J, Bentley AM, Corrigan C, Durham SR, Kay AB. Predominant TH2-like bronchoalveolar T-lymphocyte population in atopic asthma. N Engl J Med 1992; 326: 298–304
   PubMed Web of Science ®Google Scholar
• Miltenburg AM, van Laar JM, de Kuiper R, Daha MR, Breedveld FC. T cells cloned from human rheumatoid synovial membrane functionally represent the Th1 subset. Scand J Immunol 1992; 35: 603–610
   PubMed Web of Science ®Google Scholar
• Toh ML, Miossec P. The role of T cells in rheumatoid arthritis: New subsets and new targets. Curr Opin Rheumatol 2007; 19: 284–288
   PubMed Web of Science ®Google Scholar
• Szabo SJ, Jacobson NG, Dighe AS, Gubler U, Murphy KM. Developmental commitment to the Th2 lineage by extinction of IL-12 signaling. Immunity 1995; 2: 665–675
   PubMed Web of Science ®Google Scholar
• Magram J, Connaughton SE, Warrier RR, Carvajal DM, Wu CY, Ferrante J, Stewart C, Sarmiento U, Faherty DA, Gately MK. IL-12-deficient mice are defective in IFN gamma production and type 1 cytokine responses. Immunity 1996; 4: 471–481
   PubMed Web of Science ®Google Scholar
• Kopf M, Le Gros G, Bachmann M, Lamers MC, Bluethmann H, Kohler G. Disruption of the murine IL-4 gene blocks Th2 cytokine responses. Nature 1993; 362: 245–248
   PubMed Web of Science ®Google Scholar
• Zheng W, Flavell RA. The transcription factor GATA-3 is necessary and sufficient for Th2 cytokine gene expression in CD4 T cells. Cell 1997; 89: 587–596
   PubMed Web of Science ®Google Scholar
• Kurata H, Lee HJ, O'Garra A, Arai N. Ectopic expression of activated Stat6 induces the expression of Th2-specific cytokines and transcription factors in developing Th1 cells. Immunity 1999; 11: 677–688
   PubMed Web of Science ®Google Scholar
• Kaplan MH, Schindler U, Smiley ST, Grusby MJ. Stat6 is required for mediating responses to IL-4 and for development of Th2 cells. Immunity 1996; 4: 313–319
   PubMed Web of Science ®Google Scholar
• Szabo SJ, Kim ST, Costa GL, Zhang X, Fathman CG, Glimcher LH. A novel transcription factor, T-bet, directs Th1 lineage commitment. Cell 2000; 100: 655–669
   PubMed Web of Science ®Google Scholar
• Szabo SJ, Sullivan BM, Peng SL, Glimcher LH. Molecular mechanisms regulating Th1 immune responses. Annu Rev Immunol 2003; 21: 713–758
   PubMed Web of Science ®Google Scholar
• Kaplan MH, Sun YL, Hoey T, Grusby MJ. Impaired IL-12 responses and enhanced development of Th2 cells in Stat4-deficient mice. Nature 1996; 382: 174–177
   PubMed Web of Science ®Google Scholar
• Szabo SJ, Sullivan BM, Stemmann C, Satoskar AR, Sleckman BP, Glimcher LH. Distinct effects of T-bet in TH1 lineage commitment and IFN-gamma production in CD4 and CD8 T cells. Science 2002; 295: 338–342
   PubMed Web of Science ®Google Scholar
• Rao A, Avni O. Molecular aspects of T-cell differentiation. Br Med Bull 2000; 56: 969–984
   PubMed Web of Science ®Google Scholar
• Djuretic IM, Levanon D, Negreanu V, Groner Y, Rao A, Ansel KM. Transcription factors T-bet and Runx3 cooperate to activate Ifng and silence Il4 in T helper type 1 cells. Nat Immunol 2007; 8: 145–153
   PubMed Web of Science ®Google Scholar
• Bird JJ, Brown DR, Mullen AC, Moskowitz NH, Mahowald MA, Sider JR, Gajewski TF, Wang CR, Reiner SL. Helper T cell differentiation is controlled by the cell cycle. Immunity 1998; 9: 229–237
   PubMed Web of Science ®Google Scholar
• Makar KW, Wilson CB. DNA methylation is a nonredundant repressor of the Th2 effector program. J Immunol 2004; 173: 4402–4406
   PubMed Web of Science ®Google Scholar
• Hardy KJ, Manger B, Newton M, Stobo JD. Molecular events involved in regulating human interferon-gamma gene expression during T cell activation. J Immunol 1987; 138: 2353–2358
   PubMedGoogle Scholar
• Fields PE, Lee GR, Kim ST, Bartsevich VV, Flavell RA. Th2-specific chromatin remodeling and enhancer activity in the Th2 cytokine locus control region. Immunity 2004; 21: 865–876
   PubMed Web of Science ®Google Scholar
• Suck D, Oefner C. Structure of DNase I at 2.0 A resolution suggests a mechanism for binding to and cutting DNA. Nature 1986; 321: 620–625
   PubMed Web of Science ®Google Scholar
• Mullen AC, High FA, Hutchins AS, Lee HW, Villarino AV, Livingston DM, Kung AL, Cereb N, Yao TP, Yang SY, Reiner SL. Role of T-bet in commitment of TH1 cells before IL-12-dependent selection. Science 2001; 292: 1907–1910
   PubMed Web of Science ®Google Scholar
• Lee HJ, Takemoto N, Kurata H, Kamogawa Y, Miyatake S, O'Garra A, Arai N. GATA-3 induces T helper cell type 2 (Th2) cytokine expression and chromatin remodeling in committed Th1 cells. J Exp Med 2000; 192: 105–115
   Google Scholar
• Takemoto N, Arai K, Miyatake S. Cutting edge: The differential involvement of the N-finger of GATA-3 in chromatin remodeling and transactivation during Th2 development. J Immunol 2002; 169: 4103–4107
   PubMed Web of Science ®Google Scholar
• Fields PE, Kim ST, Flavell RA. Cutting edge: Changes in histone acetylation at the IL-4 and IFN-gamma loci accompany Th1/Th2 differentiation. J Immunol 2002; 169: 647–650
   PubMed Web of Science ®Google Scholar
• Avni O, Lee D, Macian F, Szabo SJ, Glimcher LH, Rao A. T (H) cell differentiation is accompanied by dynamic changes in histone acetylation of cytokine genes. Nat Immunol 2002; 3: 643–651
   PubMed Web of Science ®Google Scholar
• Mullen AC, Hutchins AS, High FA, Lee HW, Sykes KJ, Chodosh LA, Reiner SL. Hlx is induced by and genetically interacts with T-bet to promote heritable T(H)1 gene induction. Nat Immunol 2002; 3: 652–658
   PubMed Web of Science ®Google Scholar
• Zheng WP, Zhao Q, Zhao X, Li B, Hubank M, Schatz DG, Flavell RA. Up-regulation of Hlx in immature Th cells induces IFN-gamma expression. J Immunol 2004; 172: 114–122
   PubMed Web of Science ®Google Scholar
• Melvin AJ, McGurn ME, Bort SJ, Gibson C, Lewis DB. Hypomethylation of the interferon-gamma gene correlates with its expression by primary T-lineage cells. Eur J Immunol 1995; 25: 426–430
   PubMed Web of Science ®Google Scholar
• Agarwal S, Rao A. Modulation of chromatin structure regulates cytokine gene expression during T cell differentiation. Immunity 1998; 9: 765–775
   PubMed Web of Science ®Google Scholar
• Lee DU, Agarwal S, Rao A. Th2 lineage commitment and efficient IL-4 production involves extended demethylation of the IL-4 gene. Immunity 2002; 16: 649–660
   PubMed Web of Science ®Google Scholar
• Santangelo S, Cousins DJ, Winkelmann NE, Staynov DZ. DNA methylation changes at human Th2 cytokine genes coincide with DNase I hypersensitive site formation during CD4(+) T cell differentiation. J Immunol 2002; 169: 1893–1903
   PubMed Web of Science ®Google Scholar
• Young HA, Ghosh P, Ye J, Lederer J, Lichtman A, Gerard JR, Penix L, Wilson CB, Melvin AJ, McGurn ME, et al. Differentiation of the T helper phenotypes by analysis of the methylation state of the IFN-gamma gene. J Immunol 1994; 153: 3603–3610
   PubMedGoogle Scholar
• Lee GR, Fields PE, Griffin TJ, Flavell RA. Regulation of the Th2 cytokine locus by a locus control region. Immunity 2003; 19: 145–153
   PubMed Web of Science ®Google Scholar
• Spilianakis CG, Flavell RA. Long-range intrachromosomal interactions in the T helper type 2 cytokine locus. Nat Immunol 2004; 5: 1017–1027
   PubMed Web of Science ®Google Scholar
• Lee GR, Spilianakis CG, Flavell RA. Hypersensitive site 7 of the TH2 locus control region is essential for expressing TH2 cytokine genes and for long-range intrachromosomal interactions. Nat Immunol 2005; 6: 42–48
   PubMed Web of Science ®Google Scholar
• Veldhoen M, Hocking RJ, Atkins CJ, Locksley RM, Stockinger B. TGFbeta in the context of an inflammatory cytokine milieu supports de novo differentiation of IL-17-producing T cells. Immunity 2006; 24: 179–189
   PubMed Web of Science ®Google Scholar
• Stockinger B, Veldhoen M. Differentiation and function of Th17 T cells. Curr Opin Immunol 2007; 19: 281–286
   PubMed Web of Science ®Google Scholar
• Akimzhanov AM, Yang XO, Dong C. Chromatin remodeling of interleukin-17 (IL-17)-IL-17F cytokine gene locus during inflammatory helper T cell differentiation. J Biol Chem 2007; 282: 5969–5972
   PubMed Web of Science ®Google Scholar
• Bruniquel D, Schwartz RH. Selective, stable demethylation of the interleukin-2 gene enhances transcription by an active process. Nat Immunol 2003; 4: 235–240
   PubMed Web of Science ®Google Scholar
• Bird A. Il2 transcription unleashed by active DNA demethylation. Nat Immunol 2003; 4: 208–209
   Google Scholar
• Thomas RM, Gao L, Wells AD. Signals from CD28 induce stable epigenetic modification of the IL-2 promoter. J Immunol 2005; 174: 4639–4646
   PubMed Web of Science ®Google Scholar
• Sakaguchi S. Naturally arising CD4+ regulatory T cells for immunologic self-tolerance and negative control of immune responses. Annu Rev Immunol 2004; 22: 531–562
   PubMed Web of Science ®Google Scholar
• Fontenot JD, Gavin MA, Rudensky AY. Foxp3 programs the development and function of CD4+CD25+ regulatory T cells. Nat Immunol 2003; 4: 330–336
   PubMed Web of Science ®Google Scholar
• Bennett CL, Christie J, Ramsdell F, Brunkow ME, Ferguson PJ, Whitesell L, Kelly TE, Saulsbury FT, Chance PF, Ochs HD. The immune dysregulation, polyendocrinopathy, enteropathy, X-linked syndrome (IPEX) is caused by mutations of FOXP3. Nat Genet 2001; 27: 20–21
   PubMed Web of Science ®Google Scholar
• Chen W, Jin W, Hardegen N, Lei KJ, Li L, Marinos N, McGrady G, Wahl SM. Conversion of peripheral CD4+CD25 − naive T cells to CD4+CD25+ regulatory T cells by TGF-beta induction of transcription factor Foxp3. J Exp Med 2003; 198: 1875–1886
   PubMed Web of Science ®Google Scholar
• Floess S, Freyer J, Siewert C, Baron U, Olek S, Polansky J, Schlawe K, Chang HD, Bopp T, Schmitt E, Klein-Hessling S, Serfling E, Hamann A, Huehn J. Epigenetic control of the foxp3 locus in regulatory T cells. PLoS Biol 2007; 5: e38
   PubMed Web of Science ®Google Scholar
• Kim HP, Leonard WJ. CREB/ATF-dependent T cell receptor-induced FoxP3 gene expression: A role for DNA methylation. J Exp Med 2007; 204: 1543–1551
   PubMed Web of Science ®Google Scholar
• Sawalha AH, Richardson BC. DNA methylation in the pathogenesis of systemic lupus erythematosus. Curr Pharmacogenom 2005; 3: 73–78
   Google Scholar